Download Center

To set up SAW in your computer environment, follow the steps below:

• Check system requirements

• Download SAW

• Install SAW

• Download chip mask file (optional)

• Download references (optional)

System requirements

SAW pipelines on Linux systems that meet the following minimum requirements:

• 8-core Intel or AMD processor (>24 cores recommended)

• 128GB RAM (>256GB recommended)

• 1TB free disk space or higher

• 64-bit CentOS/RedHat 7.8 or Ubuntu 20.04

---

Software download

SAW 8.2.2 (Dec., 2025)

Download for Linux 64-bit (tar.gz)

File size: 8.1 GB

md5sum: 53473c7f46581c1bc088e6e6d57d8b20

wget

wget -O saw-8.2.2.tar.gz "https://enfile.stomics.tech/saw-8.2.2.tar.gz"

curl

Compatibility

• StereoMap >= v4.0 (compatibility with history versions)

SAW-8.2 highlights

• SAW makeRef

  • Support --params-config to directly input the original command lines of third-party bioinformatical tools.

  • Automatically invokes checkGTF to inspect annotation files when building STAR index files.

• SAW count/realign

  • Supports data analysis for Stereo-seq N FFPE V1.1 kit, with new analysis parameters:

    • --kit-version="Stereo-seq N FFPE V1.1"

    • --sequencing-type=PE75_50+100

  • Read alignment supports parallel computation for multiple paired/grouped FASTQ files during read alignment, to improve resource utilization and runtime efficiency.

  • Optimized analysis of RNA filtering based on specific adapter sequences, to improve the fraction of Confidently Mapped Reads.

  • --skip-cellbin helps skip image-based cell segmentation and related analysis steps.

  • --summary-display-bin-size supports effectively displaying the analysis results within the summary tabs of each omics category, chosen from [20,50,100],

  • --custom-bin-size allows custom bin sizes within the analysis pipeline. It is mainly used for secondary analysis and report presentation.

  • Introduced the Initial Check function to inspect formats of the main input datasets and software integrity before starting the analysis, with --no-initial-check to disable it.

  • --job-mode supports SGE cluster analysis, or a specific resource-configuration yaml file, enabling more refined and in-depth resource scheduling.

  • realign now supports --extra-image-enhance to set additional passes of CLAHE-based image enhancement that are applied following the default image processing. The image enhanced by this parameter is utilized for cell segmentation.

  • HTML report

    • Upgraded the UI design of the report interface, primarily including color schemes and page layouts.

    • The report content display logic has been upgraded, with the navigation bar organized according to a multimodal/multi-omics perspective. Field descriptions and explanations have been updated, and the sample information chart and the image registration check module have been added.

    • In the Microbe page, the metrics have been adjusted to display information specific to the detected tissue region.

    • In the Summary tab, the --summary-display-bin-size option is used to adjust the bin size for data display.

      In the Square Bin tab, the --custom-bin-size option is used to adjust the bin size of downstream analysis for result display.

    • In the Cell Bin tab, the cell area unit in the statistical table has been changed from pixels to μm².

    • In the ​​Square Bin and Cell Bin tabs, the report enables downsampling functionality for clustering and UMAP visualizations for large Stereo-seq chips (those with too many points during plotting).

• SAW reanalyze

  • Support spatial gene co-expression analysis.

• SAW convert

  • Support outputting RDS files for analysis in Seurat, by gef2rds, gem2rds and h5ad2rds.

  • bin2tissue can extract expression matrices based on tissue segmentation maps, and also support tissue segmentation directly based on a gene expression matrix (without images).

• Optimized log formats and content for the analysis pipeline and sub-programs.

• Enhanced error codes with more detailed and explicit error messages.

• Addition of <SN>_statistics.json file to provide comprehensive statistics for the entire analysis pipeline.

Release notes >

---

Download & installation

SAW is released as a self-contained tar.gz file that can be unpacked directly on the system, without the need to configure the computing environment. Because it has assembled all of the software-required dependencies, which are pre-compiled to run on most Linux distributions.

The reference and demo datasets need to be downloaded separately. Download the SAW software package and unpack it in a suitable location. Here sets /saw/package as the operation directory hypothetically.

$ cd /saw/package

[download the SAW package tar.gz from the Software download part]

$ tar -xzf saw-8.2.0.tar.gz

Chip mask download

The mask file of the Stereo-seq chip is essential to perform SAW count analysis. Gain more information about the Stereo-seq chip mask and learn how to download your chip mask through the tutorial.

Reference download

STOmics R&D has pre-built reference genome index files that can be used directly.

Index files for STAR alignment

Index file	Description	FIle Information
reference-data-mouse.tar.gz	Mouse reference for STAR alignment, including genome file, annotation file and index files.	File size: 27.84GB md5sum: 67c79da93b3575b31c7a97fe6e2f17f0
reference-data-mouse-rRNA.tar.gz	Mouse reference with rRNA information for STAR alignment, including genome file, annotation file and index files.	File size: 28.03GB md5sum: 6fa47b14dc26321d1cab691baee4fb2f
reference-data-rat.tar.gz	Rat reference for STAR alignment, including genome file, annotation file and index files.	File size: 27.55GB md5sum: 92dc19ab97b5ad1a16f3f1dfd34cd642
reference-data-human.tar.gz	Human reference for STAR alignment, including genome file, annotation file and index files.	File size: 31.20GB md5sum: 881b966dcd3e253cdf5ef5c36ec588dc
reference-data-human-rRNA.tar.gz	Human reference with rRNA information for STAR alignment, including genome file, annotation file and index files.	File size: 31.47GB md5sum: a86ceda324fa300d18f48b77502e5274

wget

#mouse
wget -c https://demo.stomicsdb.tech/STOmics_Reference_Released/Transcriptome/reference-data-mouse.tar.gz

#mouse with rRNA
wget -c https://demo.stomicsdb.tech/STOmics_Reference_Released/Transcriptome/reference-data-mouse-rRNA.tar.gz

#rat
wget -c https://demo.stomicsdb.tech/STOmics_Reference_Released/Transcriptome/reference-data-rat.tar.gz

#human
wget -c https://demo.stomicsdb.tech/STOmics_Reference_Released/Transcriptome/reference-data-human.tar.gz

#human with rRNA
wget -c https://demo.stomicsdb.tech/STOmics_Reference_Released/Transcriptome/reference-data-human-rRNA.tar.gz

curl

Download the reference data and unpack it in a suitable location. Here sets /saw/reference as the operation directory hypothetically.

$ cd /saw/reference

[download the mouse referencetar.gz from the reference download part]

$ tar -xzf reference-data-mouse.tar.gz

Index files for Bowtie2 alignment

Index file	Description	FIle Information
reference-data-mouse-rRNA-Bowtie2.tar.gz	Mouse reference with rRNA information for Bowtie2 alignment, including genome file and index files.	File size: 3.89GB md5sum: 2c8dd1293390009ba2a10cb28d757a74
reference-data-human-rRNA-Bowtie2.tar.gz	Human reference with rRNA information for Bowtie2 alignment, including genome file and index files.	File size: 4.32GB md5sum: 3fcc26c8df319706634514e8e5b17d73

wget

#mouse for bowtie2
wget -c https://demo.stomicsdb.tech/STOmics_Reference_Released/Transcriptome/reference-data-mouse-rRNA-Bowtie2.tar.gz

#human for bowtie2
wget -c https://demo.stomicsdb.tech/STOmics_Reference_Released/Transcriptome/reference-data-human-rRNA-Bowtie2.tar.gz

curl

Taxonomy reference for Kraken2 alignment

Index file	Description	FIle Information
reference-data-pluspf-20220908-Kraken2.tar.gz	Taxonomy reference for Kraken2 alignment.	File size: 48.47GB md5sum: 46e56a6d2707066758574d203579d1d9

wget

#kraken2 database
wget -c https://demo.stomicsdb.tech/STOmics_Reference_Released/Transcriptome/reference-data-pluspf-20220908-Kraken2.tar.gz

curl

Protein panels for PID mapping

Species	Protein panel	MD5	Cocktail information
mouse	ProteinPanel_128_mouse_V2.list	8745033762db89d5a4096232e54e6521	TotalSeq-A™ Mouse Universal Cocktail, V1.0 (Cat. No. 199901)
human	ProteinPanel_163_human_V2.list	64a20baa464ba38aa1f7f93286b18bed	TotalSeq-A™ Human Universal Cocktail, V1.0 (Cat. No. 399907)

*Know more details according to Cocktail information.

wget

#mouse
wget -c https://demo.stomicsdb.tech/STOmics_Reference_Released/Protein_Panel/ProteinPanel_128_mouse_V2.list

#human
wget -c https://demo.stomicsdb.tech/STOmics_Reference_Released/Protein_Panel/ProteinPanel_163_human_V2.list

curl

---

Access to help

Have any questions or concerns about downloads?

Please get in touch with the local agents or FAS/FBS.